FMO DATABASE

FMODB ID: 72M9K

Calculation Name: 4NEE-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NEE

Chain ID: E

ChEMBL ID:

UniProt ID: P18484

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1291082.20273
FMO2-HF: Nuclear repulsion	1235535.047022
FMO2-HF: Total energy	-55547.155708
FMO2-MP2: Total energy	-55711.463927

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(E:55:ALA)

Summations of interaction energy for fragment #1(E:55:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-15.148	-11.586	12.569	-7.087	-9.042	-0.019

Interaction energy analysis for fragmet #1(E:55:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.015

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	E	57	ALA	0	0.082	0.040	3.884	1.415	2.473	-0.006	-0.431	-0.621	0.002
4	E	58	ALA	0	-0.026	-0.007	1.845	0.466	-0.323	3.493	-1.027	-1.677	0.002
5	E	59	ALA	0	0.026	0.008	2.186	-3.627	-4.085	5.179	-2.073	-2.648	0.010
6	E	60	ALA	0	-0.056	-0.023	3.912	-1.795	-1.662	0.030	0.041	-0.204	0.002
7	E	61	ALA	0	0.004	0.023	6.836	-0.490	-0.490	0.000	0.000	0.000	0.000
8	E	72	PRO	0	-0.046	-0.043	19.617	0.015	0.015	0.000	0.000	0.000	0.000
9	E	73	GLN	0	-0.004	0.000	18.894	-0.035	-0.035	0.000	0.000	0.000	0.000
10	E	74	VAL	0	0.003	0.021	19.278	-0.030	-0.030	0.000	0.000	0.000	0.000
11	E	75	PRO	0	-0.034	-0.013	21.524	-0.008	-0.008	0.000	0.000	0.000	0.000
12	E	76	LEU	0	-0.014	-0.004	23.149	0.007	0.007	0.000	0.000	0.000	0.000
13	E	77	ARG	1	0.902	0.943	18.292	-0.229	-0.229	0.000	0.000	0.000	0.000
14	E	78	PRO	0	-0.004	0.008	23.235	0.000	0.000	0.000	0.000	0.000	0.000
15	E	79	MET	0	0.035	0.022	17.752	0.002	0.002	0.000	0.000	0.000	0.000
16	E	80	THR	0	-0.023	-0.023	21.980	-0.014	-0.014	0.000	0.000	0.000	0.000
17	E	81	TYR	0	0.004	-0.022	21.571	0.006	0.006	0.000	0.000	0.000	0.000
18	E	82	LYS	1	0.883	0.906	20.408	-0.048	-0.048	0.000	0.000	0.000	0.000
19	E	83	ALA	0	0.000	0.025	19.076	0.000	0.000	0.000	0.000	0.000	0.000
20	E	84	ALA	0	0.101	0.042	16.928	0.010	0.010	0.000	0.000	0.000	0.000
21	E	85	VAL	0	0.032	0.055	15.979	-0.032	-0.032	0.000	0.000	0.000	0.000
22	E	86	ASP	-1	-0.869	-0.914	15.700	0.014	0.014	0.000	0.000	0.000	0.000
23	E	87	LEU	0	-0.054	-0.020	12.100	0.015	0.015	0.000	0.000	0.000	0.000
24	E	88	SER	0	-0.019	-0.037	11.580	-0.029	-0.029	0.000	0.000	0.000	0.000
25	E	89	HIS	0	0.005	-0.008	10.923	-0.137	-0.137	0.000	0.000	0.000	0.000
26	E	90	PHE	0	0.008	0.027	8.611	-0.007	-0.007	0.000	0.000	0.000	0.000
27	E	91	LEU	0	0.003	-0.014	6.887	0.078	0.078	0.000	0.000	0.000	0.000
28	E	92	LYS	1	0.898	0.965	5.975	-0.020	-0.020	0.000	0.000	0.000	0.000
29	E	93	GLU	-1	-0.977	-0.995	7.559	-0.255	-0.255	0.000	0.000	0.000	0.000
30	E	94	LYS	1	0.725	0.882	3.389	-4.179	-3.695	0.019	-0.161	-0.342	0.001
31	E	95	GLY	0	0.020	0.025	3.242	-1.926	-0.498	0.054	-0.790	-0.691	-0.006
32	E	96	GLY	0	0.007	-0.040	2.407	-5.553	-4.024	3.794	-2.649	-2.674	-0.030
33	E	97	LEU	0	-0.023	-0.002	3.675	0.906	1.083	0.006	0.003	-0.185	0.000
34	E	98	GLU	-1	-0.763	-0.869	6.371	-0.363	-0.363	0.000	0.000	0.000	0.000
35	E	99	GLY	0	-0.027	-0.003	7.295	-0.152	-0.152	0.000	0.000	0.000	0.000
36	E	100	LEU	0	-0.108	-0.040	5.469	0.075	0.075	0.000	0.000	0.000	0.000
37	E	101	ILE	0	0.044	0.008	8.322	0.088	0.088	0.000	0.000	0.000	0.000
38	E	102	HIS	0	-0.036	-0.029	10.842	-0.022	-0.022	0.000	0.000	0.000	0.000
39	E	103	SER	0	0.021	0.003	12.494	0.039	0.039	0.000	0.000	0.000	0.000
40	E	104	GLN	0	-0.004	-0.024	14.080	-0.018	-0.018	0.000	0.000	0.000	0.000
41	E	105	ARG	1	0.973	0.989	11.886	0.000	0.000	0.000	0.000	0.000	0.000
42	E	106	ARG	1	0.852	0.941	7.987	0.437	0.437	0.000	0.000	0.000	0.000
43	E	107	GLN	0	0.036	0.016	11.284	0.034	0.034	0.000	0.000	0.000	0.000
44	E	108	ASP	-1	-0.806	-0.879	13.182	0.150	0.150	0.000	0.000	0.000	0.000
45	E	109	ILE	0	-0.038	-0.023	9.383	0.058	0.058	0.000	0.000	0.000	0.000
46	E	110	LEU	0	-0.026	-0.005	8.149	0.143	0.143	0.000	0.000	0.000	0.000
47	E	111	ASP	-1	-0.779	-0.896	10.914	0.153	0.153	0.000	0.000	0.000	0.000
48	E	112	LEU	0	-0.005	-0.012	14.158	0.021	0.021	0.000	0.000	0.000	0.000
49	E	113	TRP	0	0.000	0.011	9.470	0.160	0.160	0.000	0.000	0.000	0.000
50	E	114	ILE	0	0.006	0.001	11.223	0.006	0.006	0.000	0.000	0.000	0.000
51	E	115	TYR	0	-0.009	0.016	13.802	-0.035	-0.035	0.000	0.000	0.000	0.000
52	E	116	HIS	0	0.013	-0.003	15.517	-0.038	-0.038	0.000	0.000	0.000	0.000
53	E	117	THR	0	-0.063	-0.041	12.667	0.001	0.001	0.000	0.000	0.000	0.000
54	E	118	GLN	0	-0.027	-0.038	13.717	-0.085	-0.085	0.000	0.000	0.000	0.000
55	E	119	GLY	0	0.020	0.040	17.007	-0.046	-0.046	0.000	0.000	0.000	0.000
56	E	120	TYR	0	0.003	-0.006	16.717	-0.038	-0.038	0.000	0.000	0.000	0.000
57	E	121	PHE	0	0.030	0.007	19.206	0.024	0.024	0.000	0.000	0.000	0.000
58	E	122	PRO	0	-0.020	-0.003	18.092	-0.014	-0.014	0.000	0.000	0.000	0.000
59	E	123	ASP	-1	-0.872	-0.944	19.695	0.061	0.061	0.000	0.000	0.000	0.000
60	E	124	TRP	0	-0.023	-0.010	14.214	-0.034	-0.034	0.000	0.000	0.000	0.000
61	E	125	GLN	0	-0.026	0.011	13.246	-0.097	-0.097	0.000	0.000	0.000	0.000
62	E	126	ASN	0	0.021	0.005	18.428	-0.010	-0.010	0.000	0.000	0.000	0.000
63	E	127	TYR	0	-0.012	-0.036	14.753	-0.028	-0.028	0.000	0.000	0.000	0.000
64	E	128	THR	0	-0.010	-0.005	21.406	0.008	0.008	0.000	0.000	0.000	0.000
65	E	129	PRO	0	-0.009	-0.008	23.710	-0.008	-0.008	0.000	0.000	0.000	0.000
66	E	130	GLY	0	-0.007	0.038	25.302	-0.008	-0.008	0.000	0.000	0.000	0.000
67	E	131	PRO	0	-0.035	-0.035	25.711	0.010	0.010	0.000	0.000	0.000	0.000
68	E	132	GLY	0	0.001	-0.007	24.389	0.004	0.004	0.000	0.000	0.000	0.000
69	E	133	VAL	0	-0.049	-0.042	19.816	-0.006	-0.006	0.000	0.000	0.000	0.000
70	E	134	ARG	1	0.758	0.851	19.548	0.133	0.133	0.000	0.000	0.000	0.000
71	E	135	TYR	0	-0.011	-0.022	19.411	-0.030	-0.030	0.000	0.000	0.000	0.000
72	E	136	PRO	0	-0.001	0.010	18.220	0.018	0.018	0.000	0.000	0.000	0.000
73	E	137	LEU	0	0.006	-0.012	20.317	0.004	0.004	0.000	0.000	0.000	0.000
74	E	138	THR	0	-0.051	-0.030	20.139	0.012	0.012	0.000	0.000	0.000	0.000
75	E	139	PHE	0	-0.008	-0.003	20.943	-0.013	-0.013	0.000	0.000	0.000	0.000
76	E	140	GLY	0	0.046	-0.006	20.376	0.014	0.014	0.000	0.000	0.000	0.000
77	E	141	TRP	0	-0.021	-0.005	11.294	-0.001	-0.001	0.000	0.000	0.000	0.000
78	E	142	CYS	0	-0.074	-0.048	14.875	0.003	0.003	0.000	0.000	0.000	0.000
79	E	143	TYR	0	-0.011	-0.010	7.912	0.003	0.003	0.000	0.000	0.000	0.000
80	E	144	LYS	1	0.883	0.929	14.308	0.273	0.273	0.000	0.000	0.000	0.000
81	E	145	LEU	0	0.022	0.022	14.232	-0.057	-0.057	0.000	0.000	0.000	0.000
82	E	146	VAL	0	-0.014	-0.010	16.050	0.038	0.038	0.000	0.000	0.000	0.000
83	E	147	PRO	0	0.033	0.023	17.247	-0.025	-0.025	0.000	0.000	0.000	0.000
84	E	148	VAL	0	-0.029	-0.019	15.972	-0.009	-0.009	0.000	0.000	0.000	0.000
85	E	149	GLU	-1	-0.855	-0.907	18.922	-0.185	-0.185	0.000	0.000	0.000	0.000
86	E	150	PRO	0	0.069	0.016	21.346	-0.010	-0.010	0.000	0.000	0.000	0.000
87	E	151	ASP	-1	-0.827	-0.901	23.377	-0.169	-0.169	0.000	0.000	0.000	0.000
88	E	152	LYS	1	0.823	0.876	18.510	0.205	0.205	0.000	0.000	0.000	0.000
89	E	153	VAL	0	-0.008	-0.001	19.270	-0.010	-0.010	0.000	0.000	0.000	0.000
90	E	154	GLU	-1	-0.934	-0.973	20.437	-0.113	-0.113	0.000	0.000	0.000	0.000
91	E	155	GLU	-1	-0.915	-0.950	21.167	-0.147	-0.147	0.000	0.000	0.000	0.000
92	E	156	ALA	0	-0.051	-0.020	16.571	-0.004	-0.004	0.000	0.000	0.000	0.000
93	E	157	ASN	0	-0.037	-0.036	18.410	0.005	0.005	0.000	0.000	0.000	0.000
94	E	158	LYS	1	0.832	0.930	20.490	0.151	0.151	0.000	0.000	0.000	0.000
95	E	159	GLY	0	-0.010	-0.006	21.320	-0.010	-0.010	0.000	0.000	0.000	0.000
96	E	160	GLU	-1	-0.953	-0.981	23.282	-0.068	-0.068	0.000	0.000	0.000	0.000
97	E	161	ASN	0	-0.067	-0.049	20.848	0.013	0.013	0.000	0.000	0.000	0.000
98	E	162	THR	0	0.005	0.034	17.448	0.004	0.004	0.000	0.000	0.000	0.000
99	E	163	SER	0	-0.010	-0.010	16.539	0.010	0.010	0.000	0.000	0.000	0.000
100	E	164	LEU	0	0.079	0.042	18.392	-0.012	-0.012	0.000	0.000	0.000	0.000
101	E	165	LEU	0	0.002	0.002	18.148	-0.003	-0.003	0.000	0.000	0.000	0.000
102	E	166	HIS	0	-0.023	-0.003	10.966	0.030	0.030	0.000	0.000	0.000	0.000
103	E	167	PRO	0	0.005	-0.020	11.382	0.006	0.006	0.000	0.000	0.000	0.000
104	E	168	VAL	0	0.012	0.004	13.318	-0.001	-0.001	0.000	0.000	0.000	0.000
105	E	169	SER	0	0.015	-0.010	15.738	0.004	0.004	0.000	0.000	0.000	0.000
106	E	170	LEU	0	-0.068	-0.016	16.790	0.017	0.017	0.000	0.000	0.000	0.000
107	E	171	HIS	0	-0.058	-0.031	19.538	0.006	0.006	0.000	0.000	0.000	0.000
108	E	172	GLY	0	0.046	0.031	19.749	0.006	0.006	0.000	0.000	0.000	0.000
109	E	173	MET	0	-0.056	-0.020	20.445	0.013	0.013	0.000	0.000	0.000	0.000
110	E	174	ASP	-1	-0.838	-0.934	17.642	-0.050	-0.050	0.000	0.000	0.000	0.000
111	E	175	ASP	-1	-0.761	-0.841	20.712	-0.098	-0.098	0.000	0.000	0.000	0.000
112	E	176	PRO	0	0.020	0.017	22.297	0.003	0.003	0.000	0.000	0.000	0.000
113	E	177	GLU	-1	-0.911	-0.962	25.275	-0.070	-0.070	0.000	0.000	0.000	0.000
114	E	178	ARG	1	0.861	0.930	24.119	0.064	0.064	0.000	0.000	0.000	0.000
115	E	179	GLU	-1	-0.801	-0.885	21.996	-0.138	-0.138	0.000	0.000	0.000	0.000
116	E	180	VAL	0	-0.010	-0.006	17.130	-0.004	-0.004	0.000	0.000	0.000	0.000
117	E	181	LEU	0	0.002	0.013	16.543	-0.013	-0.013	0.000	0.000	0.000	0.000
118	E	182	GLU	-1	-0.834	-0.912	12.332	-0.492	-0.492	0.000	0.000	0.000	0.000
119	E	183	TRP	0	-0.023	-0.002	9.848	0.013	0.013	0.000	0.000	0.000	0.000
120	E	184	ARG	1	0.771	0.862	11.186	0.454	0.454	0.000	0.000	0.000	0.000
121	E	185	PHE	0	0.017	-0.002	11.349	0.071	0.071	0.000	0.000	0.000	0.000
122	E	186	ASP	-1	-0.825	-0.911	13.256	-0.180	-0.180	0.000	0.000	0.000	0.000
123	E	187	SER	0	0.036	0.000	16.941	0.007	0.007	0.000	0.000	0.000	0.000
124	E	188	ARG	1	0.928	0.978	18.688	0.132	0.132	0.000	0.000	0.000	0.000
125	E	189	LEU	0	0.014	0.006	17.525	0.020	0.020	0.000	0.000	0.000	0.000
126	E	190	ALA	0	0.018	0.014	19.687	0.018	0.018	0.000	0.000	0.000	0.000
127	E	191	PHE	0	-0.043	-0.011	21.501	0.017	0.017	0.000	0.000	0.000	0.000
128	E	192	HIS	0	-0.048	-0.032	24.669	0.013	0.013	0.000	0.000	0.000	0.000
129	E	193	HIS	0	0.000	0.009	24.786	-0.017	-0.017	0.000	0.000	0.000	0.000
130	E	194	VAL	0	0.034	0.005	23.962	0.006	0.006	0.000	0.000	0.000	0.000
131	E	195	ALA	0	0.028	0.024	24.235	0.004	0.004	0.000	0.000	0.000	0.000
132	E	196	ARG	1	0.928	0.970	26.152	0.030	0.030	0.000	0.000	0.000	0.000
133	E	197	GLU	-1	-0.899	-0.942	29.282	-0.067	-0.067	0.000	0.000	0.000	0.000
134	E	198	LEU	0	-0.022	-0.006	26.656	0.003	0.003	0.000	0.000	0.000	0.000
135	E	199	HIS	1	0.821	0.883	28.204	0.057	0.057	0.000	0.000	0.000	0.000
136	E	200	PRO	0	0.024	0.014	31.062	0.004	0.004	0.000	0.000	0.000	0.000
137	E	201	GLU	-1	-0.821	-0.889	33.391	-0.034	-0.034	0.000	0.000	0.000	0.000
138	E	202	TYR	0	-0.044	-0.021	28.031	0.002	0.002	0.000	0.000	0.000	0.000
139	E	203	PHE	0	-0.048	-0.011	26.578	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:55:ALA)